Merge branch 'main' of https://github.com/EarthyScience/Bigleaf.jl

Author: bgctw

.github/workflows/CI.yml

@@ -4,12 +4,17 @@ on:
     branches:
       - main
       - ci
-    tags: '*'
+    tags: ['*']
   pull_request:
+  workflow_dispatch:
 jobs:
   test:
     name: Julia ${{ matrix.group }} - ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
+    permissions: # needed to allow julia-actions/cache to proactively delete old caches that it has created
+      actions: write
+      contents: read
     strategy:
       fail-fast: false
       matrix:
@@ -18,7 +23,7 @@ jobs:
           - Basic
         version:
           - '1'
-          - '1.6' 
+          - '1.10' 
         os:
           - ubuntu-latest
         arch:
@@ -30,15 +35,6 @@ jobs:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
       - uses: julia-actions/cache@v2
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
         env:
@@ -48,27 +44,32 @@ jobs:
         with:
           file: lcov.info
           token: ${{ secrets.CODECOV_TOKEN }}
-          fail_ci_if_error: false
+          fail_ci_if_error: true
   docs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v2
-        with:
-          version: '1'
       - uses: cjdoris/julia-downgrade-compat-action@v1
-        if: ${{ matrix.version == '1.6' }}
+        if: ${{ matrix.version == '1.10' }}
         with:
           skip: Pkg,TOML,Statistics
+      - name: Configure doc environment
+        shell: julia --project=docs --color=yes {0}
+        run: |
+          using Pkg
+          Pkg.develop(PackageSpec(path=pwd()))
+          Pkg.instantiate()
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-docdeploy@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
-      - run: |
-          julia --project=docs -e '
-            using Documenter: DocMeta, doctest
+      - name: Run doctests
+        shell: julia --project=docs --color=yes {0}
+        run: |
+          using Documenter: DocMeta, doctest
             using Bigleaf
             DocMeta.setdocmeta!(Bigleaf, :DocTestSetup, :(using Bigleaf); recursive=true)
             doctest(Bigleaf)

Project.toml

@@ -39,7 +39,7 @@ StatsBase = "0.33.12, 0.34"
 Suppressor = "0.2"
 Tables = "1.6.0"
 TimeZones = "1.6.1"
-julia = "1.6"
+julia = "1.10"
 
 [workspace]
 projects = ["test", "docs"]

src/surface_roughness.jl

@@ -146,25 +146,26 @@ rp = roughness_parameters(Roughness_wind_profile(),df;zh,zr=40,d=0.8*zh)
 ≈(rp.z0m, 0.55, rtol=0.1)
 # output
 true
-``` 
-"""                                 
-function roughness_parameters(::RoughnessCanopyHeight, zh; frac_d=0.7, frac_z0m=0.1)
+```
+"""
+function roughness_parameters(::RoughnessCanopyHeight, zh::FT;
+    frac_d=FT(0.7), frac_z0m=FT(0.1)) where FT
   d      = frac_d*zh
   z0m    = frac_z0m*zh
   z0m_se = missing
   (;d, z0m, z0m_se)
 end
 
-function roughness_parameters(::RoughnessCanopyHeightLAI, zh, LAI; 
-  cd=0.2, hs=0.01)
+function roughness_parameters(::RoughnessCanopyHeightLAI, zh::FT, LAI;
+  cd=FT(0.2), hs=FT(0.01)) where FT
   X = cd * LAI
-  d = 1.1 * zh * log(1 + X^(1/4))
-  z0m = ifelse(0 <= X <= 0.2, hs + 0.3 * X^(1/2), 0.3 * zh * (1 - d/zh))
+  d = FT(1.1) * zh * log(1 + X^FT(1/4))
+  z0m = ifelse(0 <= X <= FT(0.2), hs + FT(0.3) * X^(1/2), FT(0.3) * zh * (1 - d/zh))
   z0m_se = missing
   (;d, z0m, z0m_se)
 end
 
-function roughness_parameters(::Roughness_wind_profile, ustar::AbstractVector{FT}, wind, psi_m; 
+function roughness_parameters(::Roughness_wind_profile, ustar::AbstractVector{FT}, wind, psi_m;
   zh, zr, d = 0.7*zh, constants=BigleafConstants()
   ) where FT
   FT == Missing && return((d = d, z0m = missing, z0m_se = missing))

src/unit_conversions.jl

@@ -60,17 +60,17 @@ function Esat_slope(Tair::Number; Esat_formula=Sonntag1990(), constants=BigleafC
   Delta = Esat_from_Tair_deriv(Tair; Esat_formula, constants)
   Esat, Delta
 end,
-function Esat_from_Tair(Tair; Esat_formula=Sonntag1990(), constants=BigleafConstants()) 
-  a,b,c = get_EsatCoef(Esat_formula)
-  Esat = a * exp((b * Tair) / (c + Tair)) * constants.Pa2kPa
+function Esat_from_Tair(Tair::FT; Esat_formula=Sonntag1990(), constants=BigleafConstants()) where FT
+  a,b,c = map(x -> convert(FT,x), get_EsatCoef(Esat_formula))
+  Esat = a * exp((b * Tair) / (c + Tair)) * FT(constants.Pa2kPa)
 end,
-function Esat_from_Tair_deriv(Tair; Esat_formula=Sonntag1990(), constants=BigleafConstants()) 
+function Esat_from_Tair_deriv(Tair::FT; Esat_formula=Sonntag1990(), constants=BigleafConstants()) where FT
   # slope of the saturation vapor pressure curve
   #Delta = eval(D(expression(a * exp((b * Tair) / (c + Tair))),name="Tair"))
-  a,b,c = get_EsatCoef(Esat_formula)
+  a,b,c = map(x -> convert(FT,x), get_EsatCoef(Esat_formula))
   #Delta_Pa = @. a*(b / (Tair + c) + (-Tair*b) / ((Tair + c)^2))*exp((Tair*b) / (Tair + c))
-  Delta_Pa = @. a * (exp((b * Tair)/(c + Tair)) * (b/(c + Tair) - (b * Tair)/(c + Tair)^2))
-  Delta = Delta_Pa .* constants.Pa2kPa
+  Delta_Pa = a * (exp((b * Tair)/(c + Tair)) * (b/(c + Tair) - (b * Tair)/(c + Tair)^2))
+  Delta = Delta_Pa .* FT(constants.Pa2kPa)
 end
 
 get_EsatCoef(::Sonntag1990) = (a=611.2,b=17.62,c=243.12)
@@ -145,12 +145,12 @@ true
 """
 function ms_to_mol(G_ms,Tair,pressure; constants=BigleafConstants())
   Tair     = Tair + oftype(Tair,constants.Kelvin)
-  pressure = pressure * constants.kPa2Pa 
+  pressure = pressure * oftype(Tair, constants.kPa2Pa)
   G_mol  = G_ms * pressure / (oftype(Tair, constants.Rgas)  * Tair)
 end,
 function mol_to_ms(G_mol,Tair,pressure; constants=BigleafConstants())
   Tair     = Tair + oftype(Tair,constants.Kelvin)
-  pressure = pressure * constants.kPa2Pa 
+  pressure = pressure * oftype(Tair, constants.kPa2Pa)
   G_ms  = G_mol * (oftype(Tair, constants.Rgas) * Tair) / (pressure)
 end
 

test/unit_conversions_test.jl

@@ -1,7 +1,7 @@
 using Bigleaf, Test
 
 @testset "Esat_from_Tair" begin
-  Tair = 15
+  Tair = 15.0
   Esat_formula=Sonntag1990()
   constants=BigleafConstants()
   eSat = Esat_from_Tair(Tair; Esat_formula, constants)
@@ -25,7 +25,7 @@ end
     constants=BigleafConstants()
     Esat = Esat_from_Tair.(Tair)
     delta = Esat_from_Tair_deriv.(Tair)
-    delta2 = diff(Esat)/step 
+    delta2 = diff(Esat)/step
     @test all(isapprox.(delta[2:end] - delta2, 0, atol=1e-3))
     Esat3, delta3 = Esat_slope(Tair[1])
     @test Esat3 ≈ Esat[1]